Myoglobin



Myoglobin is a globular protein whose function is to store molecular oxygen.  View1 shows a ribbon diagram, in gray, of the "Globin" (protein) portion of sperm whale deoxymyoglobin in which its eight helical segments, A through H, are displayed with two strands. Use the "zoom" slider to properly size the molecule in the viewer. Toggle the "ANIMATE" button to sequentially color these helices and their preceding nonhelical segments in rainbow order. You can see that the globin consists mostly of alpha helices; it has no beta sheets and its nonhelical segments mostly serve as links that connect the helices. Look down the barrel of some of the longer helices. Are they all straight? The heme is shown, in pink, in wireframe form with its N, O, and Fe atoms displayed as blue, red, and orange balls. Note how the heme is almost completely enclosed by the globin. Which few chemical groups of the Heme are exposed to the solvent? (Clicking on atoms displays their identity in the lower left hand corner.) Can you rationalize this exposure? View1 is the standard view of Mb. Rotate the protein around to convince yourself that the globin is approximately disc-shaped with a diameter that is about twice its thickness. Turn on the "Main Chain" button to display the polypeptide backbone in white with its N and O atoms represented by blue and red balls. How closely does the ribbon follow the main chain? Click "Animate" until the Mb ribbon is gray. Turn off the "Mb Ribbon" button. What are the orientations of the main chain carbonyl groups and the amide N atoms relative to each other which allows formation of the H-bonds of the alpha helices (not drawn)? View2 is a closeup of the heme from the same direction as View1. Turn on the "HemeLigand" button to display, in cyan, the sidechain of His 93, the proximal His, liganding the heme's Fe(II) ion (white bond). The Fe(II) is also liganded in a square-planar array by the heme's four pyrrole N atoms and hence has a total of 5 pyramidally arranged ligands. In oxyMb, the reversibly bound O2 molecule ligands the Fe from the opposite side of the heme as does the proximal His so that the Fe(II) becomes octahedrally coordinated. The Fe atom is not oxidized by its O2 ligand; it remains in the Fe(II) oxidation state. Rotate the image about the vertical axis until you see heme edge-on. Is the Heme planar? Note that the Fe atom is displaced towards the proximal His by 0.55 Å from the best plane though the porphyrin ring atoms. In oxyMb, the Fe is only 0.22 Å out of the heme plane and still on the side of the proximal His.

Exercise in large part by John H. Connor (present address: Department of Microbiology, Boston University School of Medicine, 850 Harrison Ave, Boston, MA, 02118, USA)

3D Structures of Myoglobin
Update June 2011

Myoglobin (Mb) is an oxygen binding protein found in muscle tissue. It contains a heme group. Metmyoglobin (MMb) is the oxidized form of myoglobin.

Mb wild type
2zsn, 2zso, 2zsp, 2zsq, 2zsr, 2zss, 2zst, 2zsx, 2zsy, 2zsz, 2zt0, 2zt1, 2zt2, 2zt3, 2zt4, 3e4n, 3e55, 3e5i, 3e5o, 3ecl, 3ecx, 3ecz, 3ed9, 3eda, 3edb, 2z6s, 1u7r, 1u7s, 1jp6, 1jp8, 1jp9, 1jpb, 1jw8, 1f6h, 1bz6, 1bzp, 1a6k, 1a6n, 1vxa, 1vxb, 1vxc, 1vxd, 1vxe, 1vxf, 1vxg, 1vxh, 1mlq, 1moa, 1mob, 1moc, 1mod, 4mbn, 5mbn, 1mbn – SwMb - Sperm whale

1l2k, 1cq2, 1mbd – SwMb – Neutron

1wla, 1hsy, 2v1e, 2v1f, 2v1g, 2v1h, 2v1i, 2v1j, 2v1k – hoMb - horse

2nrl – BtMb – Blackfin tuna

1mba, 3mba, 4mba – AlMb - Aplysia limacine

1m6m, 1mwd, 1mnh, 1mnj, 1mnk, 1ycb, 1pmb – pMb - pig

1lhs – stMb – sea turtle

1mbs – Mb - seal 1uvy – Mb – Paramecium caudatum

Mb mutants uncomplexed
3m38, 3m39, 3m3a, 3m3b, 3k9z, 3h57, 3h58, 2e2y, 2ef2, 2oh8, 2oh9, 2oha, 2ohb, 2blh, 2bli, 1h1x, 1co8, 1n9h, 1n9i, 1n9x, 1naz, 1f63, 1f65, 1dti, 1co9, 1cp0, 1cp5, 1cpw, 1ch1, 1ch2, 1ch3, 1ch5, 1ch7, 1ch9, 1cik, 1cio, 1ofk, 1ofj, 102m, 1obm, 2mbw, 1tes, 1irc, 1mti, 1mtj, 1mtk, 1mlf, 1mlg, 1mlh, 1mlj, 1mlk, 1mll, 1mlm, 1mlo, 1mlr, 1mln, 1mls, 2mga, 2mgb, 2mgc, 2mgd, 2mge, 2mgf, 2mgg, 2mgh, 2mgi, 2mgj, 2mgk, 2mgl, 2mgm, 2spl, 2spm, 2spn, 2spo, 1fcs, 1j52, 1lue, 1o16, 3ogb - SwMb (mutant)

2bwh - SwMb (mutant) – Laue

3hc9, 3hen, 3heo, 3hep, 1nz2, 1nz3, 1rse, 1abs, 1xch, 1hrm, 1yma - hoMb (mutant) – horse

2vlx, 2vly, 2vlz, 2vm0 – hoMb fragment

1dm1 – AlMb (mutant)

2mm1, 3rgk – hMb (mutant) – human

Mb containing a non-Fe protoporphyrin
1yog, 1yoh, 1yoi, 1myz – SwMb+Co protoporphyrin

3mn0 – SwMb (mutant)+Cu protoporphyrin+cyanide

1j3f – SwMb+Cr salophen

1ufj, 1ufp – SwMb (mutant)+Fe salophen

2o58, 2o5b – hoMb+Mn protoporphyrin

2o5l - hoMb+Mn protoporphyrin +methanol

2o5m - hoMb+Mn protoporphyrin +azide

2o5o, 2o5q - hoMb+Mn protoporphyrin +NO2

2o5s - hoMb+Co protoporphyrin +NO2

2o5t - hoMb+Co protoporphyrin

Mb+NO
1jdo, 1mlu – SwMb+NO

1hjt – SwMb (mutant)+NO

2frj, 2frk, 1npf - hoMb+NO

2nx0 – BtMb+NO

Mb+NO2
2frf, 2fri, 3lr7, 3lr9 - hoMb+NO2

Mb+O2
1ltw - SwMb (mutant)+O2

1a6m, 1mbo, 2z6s, 2z6t – SwMb+O2

1mno - pMb (mutant)+O2

Mb+CO
2bw9, 1mz0 - SwMb (mutant)+CO – Laue

2g0r, 2g0s, 2g0v, 2g0x, 2g0z, 2g10, 2g11, 2g12, 2g14, 2blj, 1dxc, 1dxd, 1do1, 1do3, 1do4, 1do7, 1abs, 1mcy, 1mbc – SwMb (mutant)+CO

1bzr, 1a6g, 1ajg, 1ajh, 1spe, 1mym, 1mbc – SwMb+CO

1myf - SwMb+CO – NMR

2mb5 - SwMb+CO – Neutron

1dwr, 1dws, 1dwt – hoMb+CO

1mdn, 1m6c – pMb (mutant)+CO

1mwc, 1yca – pMb+CO

Mb+OH
1n9f – SwMb (mutant)+OH

1gjn – hoMb+OH

Mb+cyano compounds
2jho – SwMb cyanoMet

1ebc, 2cmm - SwMb+cyanide

1iop – SwMb+cyanide+hemin

108m, 101m, 104m, 105m, 2myc, 2myd, 2mya, 2mye, 2myb – SwMb+isocyanides

103m, 107m, 111m, 106m, 109m, 110m, 112m – SwMb (mutant) +isocyanides

3ba2 – hoMb+cyanide

2fal – AlMb+cyanide

2fam – AlMb+thiocyanate

1lht – stMb+cyanide

1emy – Mb+cyanide – asian elephant

MMb
1mgn, 1duk - SwMMb

1duo – SwMMb+methyl-imidazole

1myg, 1myh, 1myi, 1myj, 1ymb – pMMb

1myt – MMb – yellowfin tuna

Other complexes of Mb
3a2g – SwMb (mutant)+fluorescein

2w6x, 2w6y - SwMb (mutant)+Xe

2w6w - SwMb +Xe

2eb8, 2eb9 – SwMb+Cu

3ase – SwMb + RuO3

2ekt, 2eku – SwMb+methyl-depropionatehemin

2d6c – SwMb+porphycene

1swm, 1mbi – SwMb+imidazole

1wvp – SwMb+tetrazolyl histidine

2evk – SwMb (mutant)+acetic acid

2evp - SwMb (mutant)+mercaptoethanol

1v9q - SwMb (mutant)+Mn salophen derivative

1dtm - SwMb (mutant)+4-methylimidazole

2nsr – hoMb+nitro methane

2nss - hoMb+nitro benzene

1azi - hoMb+azide

1bje – hoMb (mutant)+azide

1nz4 – hoMb (mutant)+Cd

1nz5 - hoMb (mutant)+Mn

2in4 - hoMb+Zn-DME

1gjn – hoMb+hydroxide

2nrm – BtMb S-nitrosylated

5mba – AlMb+azide

1mni – pMb+imidazole

apo-Mb
1bvc, 1bvd – SwApo-Mb + biliverdin